Temperature-dependent sRNA transcriptome of the Lyme disease spirochete. (December 2017)

• Record Type: Journal Article
• Authors: Popitsch, Niko; Bilusic, Ivana; Rescheneder, Philipp; Schroeder, Renée; Lybecker, Meghan
• Is Part Of: BMC genomics. Volume 18:Number 1(2017)
• Page Start: 1
• Page End: 14
• Publication Date: 2017-12
• Subjects: Borrelia burgdorferi -- sRNA transcriptome -- Regulatory RNA -- Antisense RNA (asRNA) -- Intragenic RNA (intraRNA) -- Riboswitch; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-016-3398-3
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background Transmission ofBorrelia burgdorferi from its tick vector to a vertebrate host requires extensive reprogramming of gene expression. Small regulatory RNAs (sRNA) have emerged in the last decade as important regulators of bacterial gene expression. Despite the widespread observation of sRNA-mediated gene regulation, only one sRNA has been characterized in the Lyme disease spirocheteB. burgdorferi . We employed an sRNA-specific deep-sequencing approach to identify the small RNA transcriptome ofB. burgdorferi at both 23 °C and 37 °C, which mimics in vitro the transmission from the tick vector to the mammalian host. Results We identified over 1000 sRNAs inB. burgdorferi revealing large amounts of antisense and intragenic sRNAs, as well as characteristic intergenic and 5′ UTR-associated sRNAs. A large fraction of the novel sRNAs (43%) are temperature-dependent and differentially expressed at the two temperatures, suggesting a role in gene regulation for adaptation during transmission. In addition, many genes important for maintenance ofBorrelia during its enzootic cycle are associated with antisense RNAs or 5′ UTR sRNAs. RNA-seq data were validated for twenty-two of the sRNAs via Northern blot analyses. Conclusions Our study demonstrates that sRNAs are abundant and differentially expressed by environmental conditions suggesting that gene regulation via sRNAs is a common mechanism utilized inB. burgdorferi . In addition, the identification of antisense and intragenic sRNAs impacts the broadly used loss-of-function genetic approach used to study gene function and increases the coding potential of a small genome. To facilitate access to the analyzed RNA-seq data we have set-up a website athttp://www.cibiv.at/~niko/bbdb/ that includes a UCSC browser track hub. By clicking on the respective link, researchers can interactively inspect the data in the UCSC genome browser (Kent et al., Genome Res 12:996-1006, 2002).